The following code is from the goProfiles package and works fine:

require(goProfiles)
data(prostateIds)
welsh.MF <- basicProfile(welsh01EntrezIDs, onto = "MF",level = 2, orgPackage = "org.Hs.eg.db")
singh.MF <- basicProfile(singh01EntrezIDs, onto = "MF",level = 2, orgPackage = "org.Hs.eg.db")
welsh.singh.MF <- mergeProfilesLists(welsh.MF,singh.MF, profNames = c("Welsh", "Singh"))
printProfiles(welsh.singh.MF, percentage = TRUE)

But if I load the libraries:

library(mouse4302.db)
library(annaffy)
library(annotate)
library(GSEAlm)
library(safe)

and run the above code an error is produced:

Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "toTable", for signature "environment"

> sessionInfo()
R version 2.7.0 (2008-04-22) 
x86_64-pc-linux-gnu 

locale:
C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] org.Hs.eg.db_2.2.0  goProfiles_1.2.0    safe_2.2.0         
 [4] GO_2.2.0            SparseM_0.78        GSEAlm_1.0.0       
 [7] annotate_1.18.0     xtable_1.5-2        annaffy_1.12.1     
[10] KEGG.db_2.2.0       GO.db_2.2.0         mouse4302.db_2.2.0 
[13] AnnotationDbi_1.2.1 RSQLite_0.6-8       DBI_0.2-4          
[16] Biobase_2.0.1

If I load only the libraries:

library(mouse4302.db)
library(annaffy)
library(annotate)
library(GSEAlm)

or only the library

library(safe)

the above code works.

Kind regards,
Juerg
UMASS Med School

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